The answer is 98.

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The captain says he will take 98 coins, and will give one coin to the third most senior pirate and another coin to the most junior pirate. He then explains his decision in a manner like this... If there were 2 pirates, pirate 2 being the most senior, he would just vote for himself and that would be 50% of the vote, so he's obviously going to keep all the money for himself. If there were 3 pirates, pirate 3 has to convince at least one other person to join in his plan. Pirate 3 would take 99 gold coins and give 1 coin to pirate 1. Pirate 1 knows if he does not vote for pirate 3, then he gets nothing, so obviously is going to vote for this plan. If there were 4 pirates, pirate 4 would give 1 coin to pirate 2, and pirate 2 knows if he does not vote for pirate 4, then he gets nothing, so obviously is going to vote for this plan. As there are 5 pirates, pirates 1 & 3 had obviously better vote for the captain, or they face choosing nothing or risking death.